According to Wijayawardene et al. (2018a) Hypocreales comprised nine families. Maharachchikumbura et al. (2016b) listed 223 genera belonging to families of Hypocreales based on the literature and phylogenetic analysis. Later, two new genera were introduced to Bionectriaceae: Bullanockia, and Paracylindrocarpon, based on DNA evidence and morphological data (Crous et al. 2016a, b). Corinectria, Pleiocarpon, Varicosporella and Xenoleptographium were also added in Nectriacae (González & Chaverri 2017, Aiello et al. 2017, Lechat & Fournier 2015, Crous et al. 2015d). Cryptoniesslia was introduced from previous research to Niessliaceae by Scheuer (1993) and Crous et al. (2016b) added Mycophilomyces to Clavicipitaceae. Blackwellomyces was added to Cordycipitaceae by Kepler et al. (2017). Maharachchikumbura et al. (2016b) listed seven genera in Stachybotryaceae. Lombard et al. (2016) revisited the family and 36 genera were accepted in Stachybotryaceae, including 22 new genera which based on multigene phylogeny and morphological data. Cylindriaceae, Sarocladiaceae and Xenodactylariaceae were added to the order by Crous et al. (2018a, b). However, in our phylogentic anlysis, Cylindriaceae
groups within Amphisphaeriales (Xylariomycetidae), sister to Clypeophysalosporaceae and Sporocadaceae (Figs 1, 2). Xenodactylariaceae does not appear to be related to Hypocreales as it forms a separate lineage from the order, and basal to Torpedosporales (Figs 1, 2).
Flammocladiellaceae was introduced to accommodate the monotypic genus Flammocladiella by Crous et al. (2015b). It grouped as sister clade to Clavicipitaceae with low statistical support (Crous et al. 2015b), and similar results were obtained by Maharachchikumbura et al. (2016b). Flammocladiellaceae grouped within Clavicipitaceae (Hongsanan et al. 2017, Sun et al. 2017), hence it was not accepted as a family. Hongsanan et al. (2017) treated Flammocladiellaceae under Clavicipitaceae based on phylogenetic data. However, Lechat & Fournier (2018a) observed that Flammocladiellaceae is affiliated to Bionectriaceae. In our phylogenetic analysis, Flammocladiellaceae forms a separate clade distant from Clavicipitaceae with low statistical support (Figs 1, 15). Hence, we maintain Flammocladiellaceae as a separate family in Hypocreales following Crous et al. (2015b). Here we accept 14 families in Hypocreales, namely: Bionectriaceae, Calcarisporiaceae, Clavicipitaceae, Cocoonihabitaceae, Cordycipitaceae, Flammocladiellaceae, Hypocreaceae, Myrotheciomycetaceae, Nectriaceae, Niessliaceae, Ophiocordycipitaceae, Sarocladiaceae, Stachybotryaceae, and Tilachlidiaceae, based on molecular evidence. The divergence time for Hypocreales has been estimated as 229 MYA (Fig. 2). Currently there are 303 genera in this order.

Figure 1 – Phylogram generated from maximum likelihood analysis based on combined LSU, ITS, cmdA, rpb2, tef1 and tub2 sequence data for Hypocreales. Two hundred sixty six strains are included in the combined analysis which comprised 4731 characters (890 characters for LSU, 906 characters for ITS, 557 characters for cmdA, 862 characters for rpb2, 1163 characters for tef1, 348 characters for tub2) after alignment. Single gene analyses were carried out and the phylogenies
were similar in topology and clade stability. The best RaxML tree with a final likelihood value of – 143259.087299 is presented. Estimated base frequencies were as follows: A = 0.238481, C = 0.265503, G = 0.275795, T = 0.220220; substitution rates AC = 1.361350, AG = 3.162200, AT = 1.584547, CG = 1.000927, CT = 7.415164, GT = 1.000000; gamma distribution shape parameter a = 0.592521. Bootstrap support values for ML greater than 50% are given near the nodes. The tree is rooted with Achaetomium macrosporum CBS 532.94, Chaetomium elatum CBS 374.66, Gelasinospora tetrasperma AFTOL-ID 1287, and Neurospora crassa ICMP 6360. Ex-type strains are in bold. The newly generated sequences are indicated in blue.